Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate WP_051953036.1 Q392_RS06860 glutamine amidotransferase
Query= curated2:P05379 (204 letters) >NCBI__GCF_000745855.1:WP_051953036.1 Length = 254 Score = 42.7 bits (99), Expect = 6e-09 Identities = 32/106 (30%), Positives = 45/106 (42%), Gaps = 16/106 (15%) Query: 86 PILGVCLGHQAIGAAFGGKVVPAPV-----LMHGKVSPIHHDGTGVFRGLDSPFPATRYH 140 P+LG+C GHQ + A GG+ P+ + ++ P +G + GL F A H Sbjct: 98 PVLGICYGHQLLADALGGRADDHPLGREVGTVEVELLP-EAEGDALMAGLPPRFAAQVVH 156 Query: 141 SLAVVEVPE---ALVVNAWAEEAGGRTVMGFRHRDYPTHGVQFHPE 183 + + +P AL NAW R GVQFHPE Sbjct: 157 RQSALALPPGAVALARNAWEPHQAVRF-------GEAAWGVQFHPE 195 Lambda K H 0.322 0.141 0.445 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 138 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 204 Length of database: 254 Length adjustment: 22 Effective length of query: 182 Effective length of database: 232 Effective search space: 42224 Effective search space used: 42224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory